scbi_blast 0.0.32 → 0.0.33
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- data/History.txt +4 -0
- data/lib/scbi_blast/batch_blast.rb +23 -16
- data/lib/scbi_blast.rb +1 -1
- metadata +2 -2
data/History.txt
CHANGED
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@@ -60,22 +60,9 @@ class BatchBlast
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60
60
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end
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61
61
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62
62
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cmd = get_blast_cmd(fmt)
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63
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-
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64
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-
res=
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65
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-
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66
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-
# Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando solo los 20 primeros nt.
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67
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-
IO.popen(cmd,'w+') {|blast|
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68
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-
blast.sync = true
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69
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-
blast.write(seq_fasta)
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70
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-
blast.close_write
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71
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-
res = blast.readlines
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72
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-
blast.close_read
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73
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-
}
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74
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-
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75
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-
if !$?.exitstatus.nil? && $?.exitstatus>0
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76
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raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
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77
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-
end
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78
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-
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63
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+
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64
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+
res = BatchBlast.do_blast_cmd(seq_fasta,cmd)
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65
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+
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# check if all sequences where processed
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80
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if parse_output
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81
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if fmt == :table
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@@ -101,6 +88,26 @@ class BatchBlast
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end
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end
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91
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+
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92
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return res
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93
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+
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94
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+
end
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95
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+
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96
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def self.do_blast_cmd(seq_fasta, cmd)
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97
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res=''
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+
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99
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+
# Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando solo los 20 primeros nt.
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100
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IO.popen(cmd,'w+') {|blast|
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101
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blast.sync = true
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102
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blast.write(seq_fasta)
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103
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blast.close_write
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104
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res = blast.readlines
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105
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blast.close_read
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106
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}
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107
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+
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108
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if !$?.exitstatus.nil? && $?.exitstatus>0
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109
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raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
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110
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end
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104
111
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105
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return res
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106
113
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data/lib/scbi_blast.rb
CHANGED
metadata
CHANGED
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@@ -2,7 +2,7 @@
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2
2
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name: scbi_blast
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version: !ruby/object:Gem::Version
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prerelease:
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5
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-
version: 0.0.
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5
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version: 0.0.33
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platform: ruby
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authors:
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- Dario Guerrero & Almudena Bocinos
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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13
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-
date: 2011-06
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+
date: 2011-07-06 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: hoe
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